Skip to content

Latest commit

 

History

History

data

Folders and files

NameName
Last commit message
Last commit date

parent directory

..
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Data

This directory contains working sets for h3, h1, vic and yam. These files were produced with the following pipeline:

  1. Clean sequences (remove outliers and pre-2000 sequences)
  2. Extract locations from strain names
  3. Combine locations into the 9 canonical regions
  4. Label dates as precise to the day, month or year
  5. Subsample sequences, preferring more precise dates or longer sequences

Sample counts and distributions

Full is all samples present post-2000. Small is selecting at most 14 (13 for USA) per year for H3, 30 (28 for USA) per year for H1, 30 (24 for USA) per year for Vic, 40 (25 for USA) per year for Yam. Large is selecting at most 50 (40 for USA) per year for H3, 80 (45 for USA) per year for H1, 80 (45 for USA) per year for Vic, 80 (40 for USA) per year for Yam. These sampling strategies resulting in similar overall counts across space and time.

Lineage Full Small Large
H3N2 8306 1391 4006
H1N1 3318 1372 2144
B/Vic 2247 1394 1999
B/Yam 1556 1241 1455